Cyanobacterial genome evolution subsequent to domestication by a plant (Azolla)

Larsson, John

Stockholm University, Faculty of Science, Department of Botany.

2011 (English)Doctoral thesis, comprehensive summary (Other academic)

Abstract [en]

Cyanobacteria are an ancient and globally distributed group of photosynthetic prokaryotes including species capable of fixing atmospheric dinitrogen (N2) into biologically available ammonia via the enzyme complex nitrogenase. The ability to form symbiotic interactions with eukaryotic hosts is a notable feature of cyanobacteria and one which, via an ancient endosymbiotic event, led to the evolution of chloroplasts and eventually to the plant dominated biosphere of the globe. Some cyanobacteria are still symbiotically competent and form symbiotic associations with eukaryotes ranging from unicellular organisms to complex plants. Among contemporary plant-cyanobacteria associations, the symbiosis formed between the small fast-growing aquatic fern Azolla and its cyanobacterial symbiont (cyanobiont), harboured in specialized cavities in each Azolla leaf, is the only one which is perpetual and in which the cyanobiont has lost its free-living capacity, suggesting a long-lasting co-evolution between the two partners. In this study, the genome of the cyanobiont in Azolla filiculoides was sequenced to completion and analysed. The results revealed that the genome is in an eroding state, evidenced by a high proportion of pseudogenes and transposable elements. Loss of function was most predominant in genetic categories related to uptake and metabolism of nutrients, response to environmental stimuli and in the DNA maintenance machinery. Conversely, function was retained in key symbiotic processes such as nitrogen-fixation and cell differentiation. A comparative analysis shows that the size of the cyanobiont genome has remained relatively stable, and that few genes have been completely eliminated, since the symbiotic establishment. Indications of genes acquired via horizontal gene transfer were discovered in thec yanobiont genome, some of which may have originated from the bacterial community in the Azolla leaf-cavities. It is concluded that the perpetual nature of the Azolla symbiosis has resulted in pronounced ongoing streamlining of the cyanobiont genome around core symbiotic functions, a process not described previously for complex cyanobacteria or for any bacterial plant symbiont. Further, the status of the genome indicates that the cyanobiont is at an early stage of adapting to its host-restricted environment and continued co-evolution with the plant may result in additional genome reductions. However, although a vertical transmission process is already established, the unusual extracellular location of the cyanobiont and the intricate nature of the symbiosis, may still impose restrictions on such a reductive process.

Haselkorn, Robert

Bergman, Birgitta

Abstract [en]

Background: An ancient cyanobacterial incorporation into a eukaryotic organism led to the evolution of plastids (chloroplasts) and subsequently to the origin of the plant kingdom. The underlying mechanism and the identities of the partners in this monophyletic event remain elusive.

Methodology/Principal Findings: To shed light on this evolutionary process, we sequenced the genome of a cyanobacterium residing extracellularly in an endosymbiosis with a plant, the water-fern Azolla filiculoides Lam. This symbiosis was selected as it has characters which make it unique among extant cyanobacterial plant symbioses: the cyanobacterium lacks autonomous growth and is vertically transmitted between plant generations. Our results reveal features of evolutionary significance. The genome is in an eroding state, evidenced by a large proportion of pseudogenes (31.2%) and a high frequency of transposable elements (,600) scattered throughout the genome. Pseudogenization is found in genes such as the replication initiator dnaA and DNA repair genes, considered essential to free-living cyanobacteria. For some functional categories of genes pseudogenes are more prevalent than functional genes. Loss of function is apparent even within the ‘core’ gene categories of bacteria, such as genes involved in glycolysis and nutrient uptake. In contrast, serving as a critical source of nitrogen for the host, genes related to metabolic processes such as cell differentiation and nitrogen-fixation are well preserved.

Conclusions/Significance: This is the first finding of genome degradation in a plant symbiont and phenotypically complex cyanobacterium and one of only a few extracellular endosymbionts described showing signs of reductive genome evolution. Our findings suggest an ongoing selective streamlining of this cyanobacterial genome which has resulted in an organism devoted to nitrogen fixation and devoid of autonomous growth. The cyanobacterial symbiont of Azolla can thus be considered at the initial phase of a transition from free-living organism to a nitrogen-fixing plant entity, a transition process which may mimic what drove the evolution of chloroplasts from a cyanobacterial ancestor.